(L9,10,11) Enzyme calculations and mechanisms

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How are enzymes being improved?
More active, more selective, more stable
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Give 3 examples of inhibitors
Drugs, pesticides, antibiotics
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Hydrolases
Breaks a bond using water
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Synthases
Join molecules together
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Synthetases
Join molecules together using energy from ATP hydrolysis
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Isomerases
Rearrange bonds within a single molecule
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Polymerases
Catalyse polymerisation of reactions (combine molecules to form a polymer)
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Kinase
Catalyses the addition of a phosphate
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OxidoReductases
Catalyse reduction/oxidation reactions (includes dehydrogenases)
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The rate of any enzyme mainly depends on:
Substrate concentration
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What does the Michaelis-Menten equation describe?
The kinetics of many enzymes
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v
Initial reaction velocity at specified substrate
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[S]
Substrate concentration
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Vmax
Maximum initial reaction velocity attainable by the enzyme under given conditions
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Km
Michaelis constant (When [S]=Km, v= Vmax/2)
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What are the rate constants?
K1, k-1, K2, (intermediate rate constants), the higher the rate constant, the faster the specific reaction
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First-order chemical reaction reaction rate equation
Rate= (rate constant) X (reactant concentration)
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Second-order chemical reaction rate equation
Rate= (rate constant) X (conc of reactant 1) X (conc of reactant 2)
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K2 is also known as:
Kcat (the catalytic constant)
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Assumptions of the intermediate rate constants
They define the genetics of the enzyme
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If the product is low:
Back reaction is insignificant
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Steady state:
Reaction rate is constant and therefore [ES] is constant
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Km=
(K-1+K2)/K1
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Vmax=
K2 X total enzyme conc = Kcat X total enzyme conc
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Rate of reaction depends on:
Conc of substrate and enzyme and kinetic constants for the enzyme
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Maximum rate of reaction depends on:
Concentrations of enzyme and Kcat
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At very high substrate concentrations (v=Vmax), what defines the performance of an enzyme?
Kcat
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Often substrate conc is:
Low (less than Km)
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What does rate depend on?
Ratio Kcat:Km
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When will rate be high?
Kcat is high and Km is low
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Chymotrypsin
Protease, breaks down proteins, shows side chain preference, more efficient reaction with larger side chains on amino acids
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What do inhibitors do?
Alter an enzymes kinetics
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Reversible inhibitor
Inhibitor can bind and dissociate, can be competitive non-competitive or mixed
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Irreversible inhibitor
Binds very tightly (often covalently) to the enzyme, typically inactivated enzyme
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What does the competitive inhibitor compete with?
Substrate, for binding to the enzyme
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When there is a competitive inhibitor, the Vmax is:
Unchanged because a high substrate concentration out competes the inhibitor
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When there is a competitive inhibitor, the Km is:
Raised because more substrate is needed to reach Vmax/2
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What does a non-competitive inhibitor do to the Vmax?
Decreases the Vmax
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What does a mixed inhibitor do?
Affects both Km and Vmax
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What is the double reciprocal plot?
The plot of 1/v against 1/[S], it shows the effect of an inhibitor
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On a double reciprocal plot, what crosses the X axis?
Where the line crosses the X axis shows the Km
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On a double reciprocal plot, what crosses the Y axis?
Where the line crosses the Y axis shows the Vmax
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If a line for an inhibitor crosses through the X axis at the same point the "without inhibitor" line crosses but not at the same point in the Y axis, what time of inhibitor is it?
This means the Km hasn't changed but the Vmax has so it would be a non-competitive inhibitor
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If a line for an inhibitor crosses through the Y axis at the same point the "without inhibitor" line crosses but not at the same point in the X axis, what time of inhibitor is it?
This means that the Vmax is unchanged but the Km isn't, this means that it is a competitive inhibitor
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When a chemical reaction takes place, there is:
A release or consumption of heat energy and an increase of decrease of entropy
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What is entropy?
Disorder
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What type of change is there if free energy and heat are released?
Negative
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What happened if a reaction happens spontaneously?
Releases free energy: Combination of release of heat and increase in entropy
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What does the amount of free energy depend on?
The concentrations of substrates and products, the more substrate relative to the product, the more release of free energy
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What happens when the concentrations of substrate and product are at an equilibrium?
There is no net change in their concentrations and no change in free energy
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What does the rate of reaction depend on?
Formation of transition state, which requires input of free energy
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Describe the transitional state of an amide bond (peptide bond)
Bond is flat, transitional state is a tetrahedral anion
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What is activation energy?
Free energy required to form the transition state, activation energy determines the rate of reaction
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What do catalysts do to the activation energy?
Lower it
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Describe the general mechanism of the enzyme changing the substrate to its transitional state
Enzyme orients substrate, ionic interactions between enzyme and substrate favour reaction, binding of substrate strains it into transition state, enzyme commonly form covalent bonds with substrates
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Peptidoglycan
Polymer of modified sugars with cross-linked short peptides
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What hydrolyses peptidoglycan in bacteria cell walls?
Lysozyme, substrate binds in a cleft in the lysozyme molecule
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Describe the mechanisms by which the lysozyme hydrolyses peptidoglycan
Sugar binds to enzyme, forced into strained conformation, Glu35 donates proton to sugar bond, positive charge,
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Other cards in this set

Card 2

Front

Give 3 examples of inhibitors

Back

Drugs, pesticides, antibiotics

Card 3

Front

Hydrolases

Back

Preview of the front of card 3

Card 4

Front

Synthases

Back

Preview of the front of card 4

Card 5

Front

Synthetases

Back

Preview of the front of card 5
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